arXiv subjects

Guillaume Salbreux

Publications and source records attributed to Guillaume Salbreux.

15 recordsLinked to original sources

arXiv2026

NEMO: A Framework for Nematic and Morphological Analysis of Curved and Multi-layered Biological Surfaces

Across biological scales, from cytoskeletal networks to whole tissues, orientational order and topological defects arise within complex three-dimensional geometries. However, quantifying nematic order orientational order with head-to-tail symmetry remains challenging: 2D projections introduce geometric distortions, while current 3D methods often struggle to resolve distinct nematic fields within curved or multilayer structures. Here, we introduce NEMO, a modular Python framework for the depth-resolved quantification of tangential nematic order and surface morphology. By reconstructing biological surfaces as triangulated meshes, NEMO projects curved intensity layers, extracts local nematic directors, and computes locally averaged nematic tensors within the tangent plane. The pipeline identifies topological defects and computes their topological charge by accounting for the Gaussian curvature of the underlying surface. Furthermore, NEMO quantifies tissue morphology through inter-surface distance and surface-fitted estimates of Gaussian and mean curvatures. We show the capacities of this framework using a synthetic nematic film on a vesicle and experimental actin organisation in Hydra. By combining customisable projections with surface-constrained analysis, NEMO provides a unified framework for quantifying the interplay between orientational order and geometry across scales.

cond-mat.soft↗

arXiv2024

Active morphogenesis of patterned epithelial shells

Shape transformations of epithelial tissues in three dimensions, which are crucial for embryonic development or in vitro organoid growth, can result from active forces generated within the cytoskeleton of the epithelial cells. How the interplay of local differential tensions with tissue geometry and with external forces results in tissue-scale morphogenesis remains an open question. Here, we describe epithelial sheets as active viscoelastic surfaces and study their deformation under patterned internal tensions and bending moments. In addition to isotropic effects, we take into account nematic alignment in the plane of the tissue, which gives rise to shape-dependent, anisotropic active tensions and bending moments. We present phase diagrams of the mechanical equilibrium shapes of pre-patterned closed shells and explore their dynamical deformations. Our results show that a combination of nematic alignment and gradients in internal tensions and bending moments is sufficient to reproduce basic building blocks of epithelial morphogenesis, including fold formation, budding, neck formation, flattening, and tubulation.

physics.bio-ph↗

arXiv2024

Generic theory of interacting, spinning, active polar particles: a model for cell aggregates

We present a generic framework for describing interacting, spinning, active polar particles, aimed at modelling dense cell aggregates, where cells are treated as polar, rotating objects that interact mechanically with one another and their surrounding environment. Using principles from non-equilibrium thermodynamics, we derive constitutive equations for interaction forces, torques, and polarity dynamics. We subsequently use this framework to analyse the spontaneous motion of cell doublets, uncovering a rich phase diagram of collective behaviours, including steady rotation driven by flow-polarity coupling or interactions between polarity and cell position.

cond-mat.soft↗

arXiv2023

Field theory of survival probabilities, extreme values, first passage times, and mean span of non-Markovian stochastic processes

We provide a perturbative framework to calculate extreme events of non-Markovian processes, by mapping the stochastic process to a two-species reaction diffusion process in a Doi-Peliti field theory combined with the Martin-Siggia-Rose formalism. This field theory treats interactions and the effect of external, possibly self-correlated noise in a perturbation about a Markovian process, thereby providing a systematic, diagrammatic approach to extreme events. We apply the formalism to Brownian Motion and calculate its survival probability distribution subject to self-correlated noise.

cond-mat.stat-mech↗

arXiv2022

Theory of nematic and polar active fluid surfaces

We derive a fully covariant theory of the hydrodynamics of nematic and polar active surfaces, subjected to internal and external forces and torques. We study the symmetries of polar and nematic surfaces and find that in addition to 5 different types of in-plane isotropic surfaces, polar and nematic surfaces can be classified into 5 polar, 2 pseudopolar, 5 nematic and 2 pseudonematic types of surfaces. We give examples of physical realisations of the different types of surfaces we have identified. We obtain expressions for the equilibrium tensions, moments, and external forces and torques acting on a passive polar or nematic surface. We calculate the entropy production rate using the framework of thermodynamics close to equilibrium and find constitutive equations for polar and nematic active surfaces with different symmetries. We study the instabilities of a confined flat planar-chiral polar active layer and of a confined deformable polar active surface with broken up-down symmetry.

cond-mat.soft↗

arXiv2022

Scaling of Entropy Production under Coarse Graining in Active Disordered Media

Entropy production plays a fundamental role in the study of non-equilibrium systems by offering a quantitative handle on the degree of time-reversal symmetry breaking. It depends crucially on the degree of freedom considered as well as on the scale of description. It was hitherto unknown how the entropy production at one resolution of the degrees of freedom is related to the entropy production at another resolution. This relationship is of particular relevance to coarse grained and continuum descriptions of a given phenomenon. In this work, we derive the scaling of the entropy production under iterative coarse graining on the basis of the correlations of the underlying microscopic transition rates. Our approach unveils a natural criterion to distinguish equilibrium-like and genuinely non-equilibrium macroscopic phenomena based on the sign of the scaling exponent of the entropy production per mesostate.

cond-mat.stat-mech↗

arXiv2021

Tissue hydraulics: physics of lumen formation and interaction

Lumen formation plays an essential role in the morphogenesis of tissues during development. Here we review the physical principles that play a role in the growth and coarsening of lumens. Solute pumping by the cell, hydraulic flows driven by differences of osmotic and hydrostatic pressures, balance of forces between extracellular fluids and cell-generated cytoskeletal forces, and electro-osmotic effects have been implicated in determining the dynamics and steady-state of lumens. We use the framework of linear irreversible thermodynamics to discuss the relevant force, time and length scales involved in these processes. We focus on order of magnitude estimates of physical parameters controlling lumen formation and coarsening.

cond-mat.soft↗

arXiv2021

First passage time distribution of active thermal particles in potentials

We introduce a perturbative method to calculate all moments of the first-passage time distribution in stochastic one-dimensional processes which are subject to both white and coloured noise. This class of non-Markovian processes is at the centre of the study of thermal active matter, that is self-propelled particles subject to diffusion. The perturbation theory about the Markov process considers the effect of self-propulsion to be small compared to that of thermal fluctuations. To illustrate our method, we apply it to the case of active thermal particles (i) in a harmonic trap (ii) on a ring. For both we calculate the first-order correction of the moment-generating function of first-passage times, and thus to all its moments. Our analytical results are compared to numerics.

cond-mat.stat-mech↗

arXiv2018

Stability and roughness of interfaces in mechanically-regulated tissues

Cell division and death can be regulated by the mechanical forces within a tissue. We study the consequences for the stability and roughness of a propagating interface, by analysing a model of mechanically-regulated tissue growth in the regime of small driving forces. For an interface driven by homeostatic pressure imbalance or leader-cell motility, long and intermediate-wavelength instabilities arise, depending respectively on an effective viscosity of cell number change, and on substrate friction. A further mechanism depends on the strength of directed motility forces acting in the bulk. We analyse the fluctuations of a stable interface subjected to cell-level stochasticity, and find that mechanical feedback can help preserve reproducibility at the tissue scale. Our results elucidate mechanisms that could be important for orderly interface motion in developing tissues.

physics.bio-ph↗

arXiv2017

Mechanics of active surfaces

We derive a fully covariant theory of the mechanics of active surfaces. This theory provides a framework for the study of active biological or chemical processes at surfaces, such as the cell cortex, the mechanics of epithelial tissues, or reconstituted active systems on surfaces. We introduce forces and torques acting on a surface, and derive the associated force balance conditions. We show that surfaces with in-plane rotational symmetry can have broken up-down, chiral or planar-chiral symmetry. We discuss the rate of entropy production in the surface and write linear constitutive relations that satisfy the Onsager relations. We show that the bending modulus, the spontaneous curvature and the surface tension of a passive surface are renormalised by active terms. Finally, we identify novel active terms which are not found in a passive theory and discuss examples of shape instabilities that are related to active processes in the surface.

physics.bio-ph↗

arXiv2016

Active dynamics of tissue shear flow

We present a hydrodynamic theory to describe shear flows in developing epithelial tissues. We introduce hydrodynamic fields corresponding to state properties of constituent cells as well as a contribution to overall tissue shear flow due to rearrangements in cell network topology. We then construct a generic linear constitutive equation for the shear rate due to topological rearrangements and we investigate a novel rheological behaviour resulting from memory effects in the tissue. We identify two distinct active cellular processes: generation of active stress in the tissue, and actively driven topological rearrangements. We find that these two active processes can produce distinct cellular and tissue shape changes, depending on boundary conditions applied on the tissue. Our findings have consequences for the understanding of tissue morphogenesis during development.

physics.bio-ph↗

arXiv2016

Triangles bridge the scales: Quantifying cellular contributions to tissue deformation

In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during morphogenesis of a multicellular organism. Large-scale deformations emerge from many individual cellular events such as cell shape changes, cell rearrangements, cell divisions, and cell extrusions. Using a triangle-based representation of cellular network geometry, we obtain an exact decomposition of large-scale material deformation. Interestingly, our approach reveals contributions of correlations between cellular rotations and elongation as well as cellular growth and elongation to tissue deformation. Using this Triangle Method, we discuss tissue remodeling in the developing pupal wing of the fly Drosophila melanogaster.

q-bio.TO↗

arXiv2016

Role of turn-over in active stress generation in a filament network

We study the effect of turnover of cross linkers, motors and filaments on the generation of a contractile stress in a network of filaments connected by passive crosslinkers and subjected to the forces exerted by molecular motors. We perform numerical simulations where filaments are treated as rigid rods and molecular motors move fast compared to the timescale of exchange of crosslinkers. We show that molecular motors create a contractile stress above a critical number of crosslinkers. When passive crosslinkers are allowed to turn over, the stress exerted by the network vanishes, due to the formation of clusters. When both filaments and passive crosslinkers turn over, clustering is prevented and the network reaches a dynamic contractile steady-state. A maximum stress is reached for an optimum ratio of the filament and crosslinker turnover rates.

physics.bio-ph↗

arXiv2015

Optimal chemotaxis in animal cell intermittent migration

Animal cells can sense chemical gradients without moving, and are faced with the challenge of migrating towards a target despite noisy information on the target position. Here we discuss optimal search strategies for a chaser that moves by switching between two phases of motion ("run" and "tumble"), reorienting itself towards the target during tumble phases, and performing a persistent random walk during run phases. We show that the chaser average run time can be adjusted to minimize the target catching time or the spatial dispersion of the chasers. We obtain analytical results for the catching time and for the spatial dispersion in the limits of small and large ratios of run time to tumble time, and scaling laws for the optimal run times. Our findings have implications for optimal chemotactic strategies in animal cell migration.

physics.bio-ph↗

arXiv2014

Spontaneous oscillations from turnover of an elastic contractile material

Single and collective cellular oscillations involving the actomyosin cytoskeleton have been observed in numerous biological systems. We show here that a generic model of a contractile material, which is turning over and contracts against an elastic element, exhibits spontaneous oscillations. Such a model can thus account for shape oscillations observed in amnioserosa cells during dorsal closure of the Drosophila embryo. We investigate the collective dynamics of an ensemble of such oscillators and show that the relative contribution of viscous and friction losses yield different regimes of collective oscillations. Taking into account the diffusion of contractile elements, our theoretical framework predicts the appearance of traveling waves which might account for the propagation of actomyosin contractile waves observed during morphogenesis.

physics.bio-ph↗